Monascus pigments are promising sources of natural food colorants, and their productivity can be improved by a novel extractive fermentation technology. In this study, we investigated the variations in pigment characteristics and biosynthetic gene expression levels in resting cell culture systems combined with extractive fermentation in Monascus anka GIM 3.592. Although the biomass was low at about 6 g/L DCW, high pigment titer of approximately 130 AU(470) was obtained in the resting culture with cells from extractive fermentation, illustrating that it had a good biocatalytic activity for pigment synthesis. The oxidation-reduction potential value correlated with the rate of relative content of the intracellular orange pigments to the yellow pigments (O/Y, r > 0.90, p < 0.05), indicating that the change in pigment characteristics may be responsible for the cellular redox activity. The up- or down-regulation of the pigment biosynthetic genes (MpFasA2, MpFasB2, MpPKS5, mppD, mppB, mppR1, and mppR2) in the resting culture with extractive culture cells was demonstrated by real-time quantitative polymerase chain reaction analysis. Moreover, the mppE gene associated with the yellow pigment biosynthesis was significantly (p < 0.05) down-regulated by about 18.6%, whereas the mppC gene corresponding to orange pigment biosynthesis was significantly (p < 0.05) up-regulated by approximately 21.0%. These findings indicated that extractive fermentation was beneficial for the biosynthesis of the intracellular orange pigment. The mechanism described in this study proposes a potential method for the highly efficient production of Monascus pigments.